what is the boundary condition at the end of each runner? pressure or volume flow rate? and just to confirm, you're "turning" them on and off in phase to simulate the effect of the cylinders? if you have them all open, you'll have to elaborate on how what you're trying to analyze.
what does a surface parameter of volume flow rate or pressure over time look like at each of the runner outlets? that would tell you if your boundary conditions are working properly.
what was the finishing condition that stopped your calculations? did it reach all the way to your max time?
sorry for all the questions, but when you plotted the flow trajectory, were you looking at a specific time step? if you were, you're probably only seeing what is happening with that time step vs what is happening "over time". IE, if you're turning the cylinders on and off in phase, you're only seeing what happens at one time step.